# -*- coding: utf-8 -*-
"""
**NuBio** - Data containers for bioinformatics
##############################################

The ``nubio`` package provides data-structures to store and manipulate 
biological entities i.e. sequences, alignments and molecular structures; useful
biological data e.g. genetic codes and functionsto read and write common file 
formats e.g. "pdb" or "newick". It is based on the ``NuBox`` hierarchical
array from the ``nubox`` package.

The data containers are based on a hierarchical array concept. Raw data is 
stored in a flat array, but its aspect depends on a facade object. For example 
"ATGGCG" can act as a ``NtSeq`` (sequence of 6 nucleotides) or ``CodonSeq`` 
(sequence of 2) codons. This allows to customize the behaviour of objects 
and the storage of metadata at multiple hierarchical 
levels.

The package is tested on Python 2.6+, Jython 2.5+

"""
from __future__ import (division, with_statement, absolute_import, generators,
                         nested_scopes)
from .core.aa import (Aa, AaSeq, AaAln)
from .core.atom import (Atom, AtomData, Model, ModelData)
from .core.nt import (Codon, CodonAln, CodonSeq, Nt, NtSeq, NtAln)
from .data.alphabet import (AA_IUPAC, DNA_IUPAC, RNA_IUPAC, NT_IUPAC, ANY_IUPAC,
                            GAP_IUPAC, STOP_IUPAC, AA3_TO_AA, AA_TO_AA3, GENETIC_CODE_STANDARD)
from .data.score import (BLOSUM62, PAM250)
from .io.fasta import (fasta_seq_parser, fasta_seq_writer,
                       fasta_aln_parser, fasta_aln_writer,
                       fasta_tmp)
from .io.pdb import (pdb_parser, pdb_writer, pdb_tmp)
from .io.stockholm import (stockholm_aln_parser, stockholm_aln_writer, stockholm_tmp)
#from .io.jalview import (jalview_annotation_writer, jalview_feature_writer,
#                         jalview_graph_writer)
# from .io.newick import (newick_writer,)


